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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ), 'gf_id' => 'HOM05D001202', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001202' ), 'data_identifier' => 'HOM05D001202', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001202', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '520', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p49760' => 'bna', 'A07p18590' => 'bna', 'A08p12270' => 'bna', 'A10p18890' => 'bna', 'Aa31LG2G12420' => 'aar', 'Aa31LG5G8090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5152' => 'aag', 'Actinidia02286' => 'ach', 'Actinidia06996' => 'ach', 'Actinidia07164' => 'ach', 'Actinidia07867' => 'ach', 'Actinidia24127' => 'ach', 'Ah.01g003120' => 'amhyb', 'Ah.01g014180' => 'amhyb', 'Ah.01g014830' => 'amhyb', 'Ah.09g233920' => 'amhyb', 'AL4G22120' => 'aly', 'AL6G32790' => 'aly', 'AL7G38680' => 'aly', 'Aqoxy1G00020' => 'aox', 'Aqoxy1G01169' => 'aox', 'Aqoxy4G02340' => 'aox', 'Aqoxy579s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3X6SQ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6I306W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.93CGGZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB8LVY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HQ9GR2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MH0DCU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NYNB9A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P9LE7G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNQ63J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SU4MJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TSL6B6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WWBH0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XVLR9R' => 'arhy', 'AT2G28060' => 'ath', 'AT5G21170' => 'ath', 'ATR0680G193' => 'atr', 'ATR0827G119' => 'atr', 'ATR1096G035' => 'atr', 'Atru.chr1.2277' => 'acertr', 'Atru.chr3.2928' => 'acertr', 'Atru.chr3.3563' => 'acertr', 'Atru.chr6.3395' => 'acertr', 'AUR62012841' => 'cqu', 'AUR62021818' => 'cqu', 'AUR62022767' => 'cqu', 'AUR62025114' => 'cqu', 'AUR62029218' => 'cqu', 'AUR62037163' => 'cqu', 'BcaB02g10134' => 'bca', 'BcaB04g18378' => 'bca', 'BcaB05g22767' => 'bca', 'BcaB08g36480' => 'bca', 'BcaC02g10936' => 'bca', 'BcaC04g19517' => 'bca', 'BcaC06g33476' => 'bca', 'BcaC07g37978' => 'bca', 'BcaNung06745' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01050' => 'bna', 'BolC2t07111H' => 'bol', 'BolC4t23853H' => 'bol', 'BolC7t45304H' => 'bol', 'BolC8t48360H' => 'bol', 'BolC9t58350H' => 'bol', 'BraA02t05623Z' => 'bra', 'BraA03t14072Z' => 'bra', 'BraA07t29571Z' => 'bra', 'BraA08t33231Z' => 'bra', 'BraA10t43968Z' => 'bra', 'C04p23500' => 'bna', 'C07p47820' => 'bna', 'C09p54890' => 'bna', 'CAN.G1156.15' => 'can', 'CAN.G171.4' => 'can', 'CAN.G177.9' => 'can', 'CAN.G309.18' => 'can', 'CAN.G449.31' => 'can', 'CAN.G484.13' => 'can', 'CANSAT54G1274' => 'cansat', 'CANSAT54G1376' => 'cansat', 'CANSAT56G3013' => 'cansat', 'CANSAT64G0518' => 'cansat', 'CARHR120760' => 'chi', 'CARHR191700' => 'chi', 'CARHR222730' => 'chi', 'Carub.0004s0881' => 'cru', 'Carub.0006s1948' => 'cru', 'Carub.0007s2517' => 'cru', 'Ca_01390_v3' => 'car', 'Ca_06165_v3' => 'car', 'Ca_20997_v3' => 'car', 'CBR_g4892' => 'cbr', 'Cc01_g06750' => 'ccan', 'Cc01_g10660' => 'ccan', 'Cc09_g00380' => 'ccan', 'Cc09_g00390' => 'ccan', 'CDE02G4068' => 'cde', 'CDE08G0246' => 'cde', 'CDE08G0356' => 'cde', 'Cfa010274' => 'cfa', 'Cfa014226' => 'cfa', 'Cfa023394' => 'cfa', 'Ciclev10016186m.g' => 'ccl', 'Ciclev10016199m.g' => 'ccl', 'Ciclev10016448m.g' => 'ccl', 'Ciclev10029607m.g' => 'ccl', 'CiPaw.03G281700' => 'cil', 'CiPaw.09G108400' => 'cil', 'CiPaw.10G081400' => 'cil', 'CiPaw.13G117700' => 'cil', 'CiPaw.14G089400' => 'cil', 'ClCG01G010780' => 'cla', 'ClCG01G021250' => 'cla', 'ClCG02G002880' => 'cla', 'ClCG02G009220' => 'cla', 'ClCG02G021380' => 'cla', 'ClCG03G014360' => 'cla', 'COL.COLO4_18344' => 'col', 'COL.COLO4_31934' => 'col', 'COL.COLO4_33328' => 'col', 'COL.COLO4_34711' => 'col', 'Cpa.g.sc136.29' => 'cpa', 'Cpa.g.sc27.236' => 'cpa', 'Cpa.g.sc34.219' => 'cpa', 'Cre10.g457500' => 'cre', 'CsaV3_1G015740' => 'csa', 'CsaV3_1G041860' => 'csa', 'CsaV3_3G023540' => 'csa', 'CsaV3_4G009170' => 'csa', 'CsaV3_6G009600' => 'csa', 'CsaV3_6G014170' => 'csa', 'CsaV3_6G048260' => 'csa', 'CsaV3_7G002490' => 'csa', 'CSS0000633' => 'camsi', 'CSS0018484' => 'camsi', 'CSS0022763' => 'camsi', 'CSS0025516' => 'camsi', 'CSS0025695' => 'camsi', 'CSS0035423' => 'camsi', 'CSS0035651' => 'camsi', 'CSS0036190' => 'camsi', 'CSS0040074' => 'camsi', 'CSS0048091' => 'camsi', 'DCAR_002242' => 'dca', 'DCAR_006082' => 'dca', 'DCAR_006087' => 'dca', 'DCAR_015517' => 'dca', 'DCAR_018972' => 'dca', 'DCAR_025227' => 'dca', 'DCAR_030836' => 'dca', 'Dinv04398' => 'din', 'Dinv10715' => 'din', 'Dinv21297' => 'din', 'Dinv26605' => 'din', 'Dinv29352' => 'din', 'Dinv34694' => 'din', 'Duzib138G1696' => 'dzi', 'Duzib150G0408' => 'dzi', 'Duzib150G0924' => 'dzi', 'Duzib160G0433' => 'dzi', 'Duzib168G1552' => 'dzi', 'Duzib168G1572' => 'dzi', 'Duzib168G1648' => 'dzi', 'Duzib170G0554' => 'dzi', 'Duzib192G0203' => 'dzi', 'Duzib211G0629' => 'dzi', 'Duzib235G0098' => 'dzi', 'ECA234G1778' => 'eca', 'ECA234G4594' => 'eca', 'ECA240G4489' => 'eca', 'ECA246G0015' => 'eca', 'EL10Ac8g20258' => 'bvu', 'EL10Ac9g22373' => 'bvu', 'EL10Ac9g22567' => 'bvu', 'Eucgr.H00877' => 'egr', 'Eucgr.J00639' => 'egr', 'Eucgr.J00900' => 'egr', 'Eucgr.L00156' => 'egr', 'FAN02G4220' => 'fan', 'FAN05G0883' => 'fan', 'FAN05G3299' => 'fan', 'FAN05G4807' => 'fan', 'FAN09G2306' => 'fan', 'FAN14G4801' => 'fan', 'FAN16G0021' => 'fan', 'FAN19G0587' => 'fan', 'FAN21G2257' => 'fan', 'FAN21G3748' => 'fan', 'FAN23G2329' => 'fan', 'FAN24G3219' => 'fan', 'FAN25G0082' => 'fan', 'FAN25G1905' => 'fan', 'FAN25G3004' => 'fan', 'FAN26G1313' => 'fan', 'FAN26G3255' => 'fan', 'FvH4_1g28790' => 'fve', 'FvH4_3g00390' => 'fve', 'FvH4_3g31260' => 'fve', 'FvH4_6g40620' => 'fve', 'Glyma.02G275500' => 'gma', 'Glyma.02G308800' => 'gma', 'Glyma.07G267900' => 'gma', 'Glyma.09G013900' => 'gma', 'Glyma.11G195300' => 'gma', 'Glyma.12G078800' => 'gma', 'Glyma.14G004100' => 'gma', 'Glyma.14G040700' => 'gma', 'Glyma.15G118600' => 'gma', 'Glyma.17G006000' => 'gma', 'Gohir.A03G031400' => 'ghi', 'Gohir.A03G064250' => 'ghi', 'Gohir.A05G102300' => 'ghi', 'Gohir.A06G204200' => 'ghi', 'Gohir.A07G192000' => 'ghi', 'Gohir.A08G197100' => 'ghi', 'Gohir.A08G199800' => 'ghi', 'Gohir.D03G137000' => 'ghi', 'Gohir.D05G102000' => 'ghi', 'Gohir.D06G217300' => 'ghi', 'Gohir.D07G198300' => 'ghi', 'Gohir.D08G214300' => 'ghi', 'Gohir.D08G216900' => 'ghi', 'Gohir.D10G134000' => 'ghi', 'Gohir.D11G177400' => 'ghi', 'Gohir.D13G084860' => 'ghi', 'Gohir.D13G118800' => 'ghi', 'Gohir.D13G237800' => 'ghi', 'Gorai.001G221900' => 'gra', 'Gorai.001G222000' => 'gra', 'Gorai.003G144000' => 'gra', 'Gorai.004G228400' => 'gra', 'Gorai.004G230600' => 'gra', 'Gorai.009G106200' => 'gra', 'Gorai.010G248900' => 'gra', 'Gorai.013G096700' => 'gra', 'Gorai.013G268600' => 'gra', 'GSVIVG01005134001' => 'vvi', 'GSVIVG01005136001' => 'vvi', 'GSVIVG01031523001' => 'vvi', 'GSVIVG01037416001' => 'vvi', 'HanXRQChr03g0075151' => 'han', 'HanXRQChr13g0419321' => 'han', 'HanXRQChr16g0515791' => 'han', 'HanXRQChr17g0558141' => 'han', 'Haze_07012' => 'cav', 'Haze_12629' => 'cav', 'Haze_23690' => 'cav', 'Haze_23764' => 'cav', 'Hma1.2p1_0218F.1_g092810' => 'hma', 'Hma1.2p1_0344F.1_g131160' => 'hma', 'Hma1.2p1_0344F.1_g131165' => 'hma', 'Hma1.2p1_0545F.1_g175910' => 'hma', 'Hma1.2p1_1175F.1_g263960' => 'hma', 'HPP92_000649' => 'vpl', 'HPP92_000697' => 'vpl', 'HPP92_005754' => 'vpl', 'HPP92_005756' => 'vpl', 'HPP92_005825' => 'vpl', 'Hund01338' => 'sun', 'Hund14843' => 'sun', 'Lalb_Chr03g0027591' => 'lal', 'Lalb_Chr04g0249581' => 'lal', 'Lalb_Chr10g0105981' => 'lal', 'Lalb_Chr12g0195961' => 'lal', 'Lalb_Chr15g0088191' => 'lal', 'Lalb_Chr17g0347611' => 'lal', 'Lalb_Chr17g0349311' => 'lal', 'Lalb_Chr18g0057261' => 'lal', 'Lalb_Chr18g0057271' => 'lal', 'Lalb_Chr19g0137031' => 'lal', 'Lj1A796T38' => 'lonja', 'Lj2A257T61' => 'lonja', 'Lj2A936G15' => 'lonja', 'Lj2C257T7' => 'lonja', 'Lj3g0022217' => 'lja', 'Lj6g0018645' => 'lja', 'LjContig00081g0009195' => 'lja', 'LjContig00564g0024500' => 'lja', 'Lsat_1_v5_gn_4_23520' => 'lsa', 'Lsat_1_v5_gn_4_63801' => 'lsa', 'Lsat_1_v5_gn_9_103900' => 'lsa', 'Manes.01G002051' => 'mes', 'Manes.04G016000' => 'mes', 'Manes.08G069900' => 'mes', 'Manes.11G111100' => 'mes', 'Manes.12G065600' => 'mes', 'Manes.13G062000' => 'mes', 'Mapoly0002s0309' => 'mpo', 'Mapoly0071s0044' => 'mpo', 'Mapoly0126s0042' => 'mpo', 'Mapoly0126s0043' => 'mpo', 'Mapoly0126s0046' => 'mpo', 'Mapoly0158s0025' => 'mpo', 'Mapoly1745s0001' => 'mpo', 'MBI13_g31588_MAGBIO' => 'mbi', 'MBI13_g32098_MAGBIO' => 'mbi', 'MBI16_g22135_MAGBIO' => 'mbi', 'MBI18_g25258_MAGBIO' => 'mbi', 'MBI19_g10812_MAGBIO' => 'mbi', 'MCO01G321' => 'mco', 'MD03G1124800' => 'mdo', 'MD05G1360800' => 'mdo', 'MD09G1126700' => 'mdo', 'MD10G1338400' => 'mdo', 'MD11G1141500' => 'mdo', 'MD15G1312500' => 'mdo', 'MD17G1117000' => 'mdo', 'Medtr0446s0050' => 'mtr', 'Medtr2g026695' => 'mtr', 'Medtr2g095290' => 'mtr', 'Medtr4g133970' => 'mtr', 'Medtr5g088270' => 'mtr', 'Medtr5g098510' => 'mtr', 'MELO3C008009.2' => 'cme', 'MELO3C015601.2' => 'cme', 'MELO3C024193.2' => 'cme', 'MELO3C025522.2' => 'cme', 'MELO3C025960.2' => 'cme', 'MELO3C026917.2' => 'cme', 'Migut.D00692' => 'egut', 'Migut.H01627' => 'egut', 'Migut.M01441' => 'egut', 'Migut.N02579' => 'egut', 'MSTRG.13108' => 'ama', 'MSTRG.16051' => 'ama', 'MSTRG.18681' => 'ama', 'MSTRG.21101' => 'ama', 'MSTRG.21329' => 'ama', 'MSTRG.7133' => 'ama', 'Nitab4.5_0000181g0210' => 'nta', 'Nitab4.5_0000870g0010' => 'nta', 'Nitab4.5_0001296g0070' => 'nta', 'Nitab4.5_0001701g0210' => 'nta', 'Nitab4.5_0001867g0120' => 'nta', 'Nitab4.5_0001904g0060' => 'nta', 'Nitab4.5_0001925g0200' => 'nta', 'Nitab4.5_0002478g0060' => 'nta', 'Nitab4.5_0002693g0040' => 'nta', 'Nitab4.5_0003533g0080' => 'nta', 'Nn1g03192' => 'nnu', 'Nn2g11567' => 'nnu', 'Nn2g13765' => 'nnu', 'Nn7g37207' => 'nnu', 'Oeu002778.1' => 'oeu', 'Oeu014009.1' => 'oeu', 'Oeu018376.1' => 'oeu', 'Oeu025399.1' => 'oeu', 'Oeu032032.1' => 'oeu', 'Oeu044428.1' => 'oeu', 'Oeu044429.1' => 'oeu', 'Oeu057023.1' => 'oeu', 'Os03g0319100' => 'osa', 'Os05g0491200' => 'osa', 'Os07g0687300' => 'osa', 'Os09g0364900' => 'osa', 'Peaxi162Scf00062g00921' => 'pax', 'Peaxi162Scf00115g00062' => 'pax', 'Peaxi162Scf00442g00711' => 'pax', 'Peaxi162Scf00576g00121' => 'pax', 'Peaxi162Scf00802g00238' => 'pax', 'PGR004G2341' => 'pgr', 'PGR083G0688' => 'pgr', 'PGR119G0817' => 'pgr', 'PGR119G2560' => 'pgr', 'PGSC0003DMG400001146' => 'stu', 'PGSC0003DMG400004655' => 'stu', 'PGSC0003DMG400005545' => 'stu', 'PGSC0003DMG400008440' => 'stu', 'PGSC0003DMG400013299' => 'stu', 'PGSC0003DMG400015733' => 'stu', 'PGSC0003DMG400017398' => 'stu', 'Phvul.003G086600' => 'pvu', 'Phvul.006G139600' => 'pvu', 'Phvul.008G206100' => 'pvu', 'Phvul.008G288900' => 'pvu', 'Phvul.011G083400' => 'pvu', 'Potri.001G220800' => 'ptr', 'Potri.004G213600' => 'ptr', 'Potri.006G005800' => 'ptr', 'Potri.009G008700' => 'ptr', 'Potri.009G021600' => 'ptr', 'Potri.014G167400' => 'ptr', 'Potri.016G006400' => 'ptr', 'Pp3c12_8780' => 'ppa', 'Pp3c4_19530' => 'ppa', 'PRCOL_00002369' => 'pco', 'Prupe.3G197500' => 'ppe', 'Prupe.4G004500' => 'ppe', 'Prupe.6G107300' => 'ppe', 'Psat0s2281g0200' => 'psa', 'Psat1g172880' => 'psa', 'Psat2g002480' => 'psa', 'Psat2g050160' => 'psa', 'Psat4g002960' => 'psa', 'Psat5g280640' => 'psa', 'PSO063G3956' => 'pso', 'PSO339G1837' => 'pso', 'PSO384G0704' => 'pso', 'PSO675G1580' => 'pso', 'QL01p007443' => 'qlo', 'QL01p007448' => 'qlo', 'QL01p020749' => 'qlo', 'QL04p068501' => 'qlo', 'QL04p089700' => 'qlo', 'QL05p067849' => 'qlo', 'QL09p001089' => 'qlo', 'RcHm_v2.0_Chr2g0155991' => 'rch', 'RcHm_v2.0_Chr5g0000591' => 'rch', 'RcHm_v2.0_Chr5g0050101' => 'rch', 'RcHm_v2.0_Chr5g0057871' => 'rch', 'Rhsim02G0200200' => 'rsi', 'Rhsim06G0176500' => 'rsi', 'Rhsim13G0141200' => 'rsi', 'Rhsim13G0141300' => 'rsi', 'Rhsim13G0201600' => 'rsi', 'Sabra04G0144900' => 'sbr', 'Sabra06G0004700' => 'sbr', 'Sabra09G0005100' => 'sbr', 'Sabra09G0013300' => 'sbr', 'Sabra14G0127400' => 'sbr', 'Sabra16G0011200' => 'sbr', 'Sabra16G0123700' => 'sbr', 'Sabra16G0131500' => 'sbr', 'SalBow3G1107' => 'sbo', 'SalBow3G1558' => 'sbo', 'SalBow8G2450' => 'sbo', 'Sc05g0009830' => 'sci', 'Sc06g0010400' => 'sci', 'Sc21g0000270' => 'sci', 'Sed0005876' => 'sed', 'Sed0006265' => 'sed', 'Sed0009781' => 'sed', 'Sed0012686' => 'sed', 'Sed0012742' => 'sed', 'Sed0013703' => 'sed', 'Sed0019729' => 'sed', 'Sed0024777' => 'sed', 'Sed0025887' => 'sed', 'Sed0026569' => 'sed', 'SEGI_21925' => 'sgi', 'SGA_v2.0_scaffold127G34038' => 'sas', 'SGA_v2.0_scaffold186G40119' => 'sas', 'SGA_v2.0_scaffold239G43971' => 'sas', 'SGA_v2.0_scaffold29G12177' => 'sas', 'SHI04456' => 'shi', 'SHI25152' => 'shi', 'SMO116G0269' => 'smo', 'Solyc05g054220.3' => 'sly', 'Solyc06g010260.3' => 'sly', 'Solyc07g045460.3' => 'sly', 'Solyc11g012710.2' => 'sly', 'Solyc11g069765.1' => 'sly', 'Solyc12g099970.2' => 'sly', 'Sopen05g032710' => 'spe', 'Sopen06g005220' => 'spe', 'Sopen07g024000' => 'spe', 'Sopen11g007450' => 'spe', 'Sopen11g028520' => 'spe', 'Sopen12g034590' => 'spe', 'Sp4g10840' => 'spa', 'Sp6g23350' => 'spa', 'Sp7g14880' => 'spa', 'TAR369G0219' => 'tar', 'TAR623G0112' => 'tar', 'TAR623G0963' => 'tar', 'TAR624G1362' => 'tar', 'TAR626G1827' => 'tar', 'TAR629G2184' => 'tar', 'TAR629G3175' => 'tar', 'TAR633G2453' => 'tar', 'TAR633G2710' => 'tar', 'TAR636G1760' => 'tar', 'TAR636G2020' => 'tar', 'THA.LOC104800588' => 'tha', 'THA.LOC104810958' => 'tha', 'THA.LOC104812784' => 'tha', 'THA.LOC104814479' => 'tha', 'Thecc.01G196000' => 'tca', 'Thecc.06G240100' => 'tca', 'Thecc.09G339400' => 'tca', 'Thecc.09G347200' => 'tca', 'Thhalv10014317m.g' => 'esa', 'Thhalv10017447m.g' => 'esa', 'Thhalv10025902m.g' => 'esa', 'TPR.G10576' => 'tpr', 'TPR.G11308' => 'tpr', 'TPR.G34417' => 'tpr', 'TPR.G35898' => 'tpr', 'TPR.G5771' => 'tpr', 'TPR.G5985' => 'tpr', 'TWI18G1386' => 'twi', 'TWI31G0264' => 'twi', 'TWI36G0328' => 'twi', 'TWI63G0547' => 'twi', 'TWI75G0687' => 'twi', 'TWI79G0587' => 'twi', 'TWI79G0847' => 'twi', 'unitig_578.g16663' => 'ugi', 'unitig_736.g22406' => 'ugi', 'unitig_749.g13687' => 'ugi', 'unitig_899.g14929' => 'ugi', 'vmacro03276' => 'vma', 'vmacro03614' => 'vma', 'vmacro04100' => 'vma', 'vmacro12083' => 'vma', 'VMungo0540G1650' => 'vmu', 'VMungo0647G0332' => 'vmu', 'VMungo0647G1901' => 'vmu', 'VMungo1127G0637' => 'vmu', 'VMungo1215G0007' => 'vmu', 'Zm00001eb015170' => 'zma', 'Zm00001eb035630' => 'zma', 'Zm00001eb138860' => 'zma', 'Zm00001eb138870' => 'zma', 'Zm00001eb139330' => 'zma', 'Zm00001eb331190' => 'zma', 'Zm00001eb352470' => 'zma', 'Zm00001eb395720' => 'zma' ) $gf_id = 'HOM05D001202' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001202' ) $data_identifier = 'HOM05D001202' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 13, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 6, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 8, 'camsi' => (int) 10, 'dca' => (int) 7, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 10, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 7, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 6, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 7, 'pvu' => (int) 5, 'ptr' => (int) 7, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 10, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 11, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395720' $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